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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 27 November 2012, Vol.109(48), pp.19563-8
    Description: The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k(B)T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (〉20 k(B)T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues.
    Keywords: Protein Folding ; Proteins -- Chemistry
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Ecological Modelling, Nov 10, 2013, Vol.269, p.98(15)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ecolmodel.2013.08.013 Byline: Michael Strauch, Martin Volk Abstract: acents The SWAT plant growth module was adapted for improved simulations in Central Brazil. acents Simulated soil moisture is used to provoke new growing cycles. acents Logistic decline rate for LAI is used to consider specific minimum LAI values. acents Simulated LAI and ET were successfully proven based on MODIS reference data. acents Implemented new model parameters allow application in other tropical regions. Author Affiliation: (a) UFZ - Helmholtz Centre for Environmental Research, Department of Computational Landscape Ecology, Permoserstra[sz]e 15, 04318 Leipzig, Germany (b) Institute of Soil Science and Site Ecology, TU Dresden, Pienner Stra[sz]e 19, 01737 Tharandt, Germany Article History: Received 2 July 2013; Revised 22 August 2013; Accepted 23 August 2013
    Keywords: Soil Moisture -- Analysis ; Soil Moisture -- Models
    ISSN: 0304-3800
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Environmental Management, 2010, Vol.46(6), pp.834-849
    Description: This article analyses the benefits and shortcomings of the recently developed decision support systems (DSS) FLUMAGIS, Elbe-DSS, CatchMODS, and MedAction. The analysis elaborates on the following aspects: (i) application area/decision problem, (ii) stakeholder interaction/users involved, (iii) structure of DSS/model structure, (iv) usage of the DSS, and finally (v) most important shortcomings. On the basis of this analysis, we formulate four criteria that we consider essential for the successful use of DSS in landscape and river basin management. The criteria relate to (i) system quality, (ii) user support and user training, (iii) perceived usefulness and (iv) user satisfaction. We can show that the availability of tools and technologies for DSS in landscape and river basin management is good to excellent. However, our investigations indicate that several problems have to be tackled. First of all, data availability and homogenisation, uncertainty analysis and uncertainty propagation and problems with model integration require further attention. Furthermore, the appropriate and methodological stakeholder interaction and the definition of ‘what end-users really need and want’ have been documented as general shortcomings of all four examples of DSS. Thus, we propose an iterative development process that enables social learning of the different groups involved in the development process, because it is easier to design a DSS for a group of stakeholders who actively participate in an iterative process. We also identify two important lines of further development in DSS: the use of interactive visualization tools and the methodology of optimization to inform scenario elaboration and evaluate trade-offs among environmental measures and management alternatives.
    Keywords: Decision support systems ; Models ; Optimization ; Landscape management ; River basin management ; Environmental policy ; Model integration
    ISSN: 0364-152X
    E-ISSN: 1432-1009
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  • 4
    In: PLoS ONE, 2017, Vol.12(12)
    Description: Over the 20 th century, urbanization has substantially shaped the surface of Earth. With population rapidly shifting from rural locations towards the cities, urban areas have dramatically expanded on a global scale and represent crystallization points of social, cultural and economic assets and activities. This trend is estimated to persist for the next decades, and particularly the developing countries are expected to face rapid urban growth. The management of this growth will require good governance strategies and planning. By threatening the livelihoods, assets and health as foundations of human activities, another major global change contributor, climate change, became an equally important concern of stakeholders. Based on the climate trends observed over the 20 th century, and a spatially explicit model of urbanization, this paper investigates the impacts of climate change in relation to different stages of development of urban areas, thus evolving a more integrated perspective on both processes. As a result, an integrative measure of climate change trends and impacts is proposed and estimated for urban areas worldwide. We show that those areas facing major urban growth are to a large extent also hotspots of climate change. Since most of these hotspots are located in the Global South, we emphasize the need for stakeholders to co-manage both drivers of global change. The presented integrative perspective is seen as a starting point to foster such co-management, and furthermore as a means to facilitate communication and knowledge exchange on climate change impacts.
    Keywords: Research Article ; Earth Sciences ; Physical Sciences ; Earth Sciences ; Ecology And Environmental Sciences ; Earth Sciences ; Earth Sciences ; Ecology And Environmental Sciences ; People And Places
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: Ecological Modelling, 10 November 2013, Vol.269, pp.98-112
    Description: The Soil and Water Assessment Tool (SWAT) has been used for assessing the impact of land cover and land management changes on water resources for a wide range of scales and environmental conditions across the globe. However, originally designed for temperate regions, SWAT must be critically examined for its appropriate use in tropical watersheds. One major concern is the simulation of perennial tropical vegetation due to the absence of dormancy. While for temperate regions SWAT uses dormancy to terminate growing seasons of trees and perennials, seasonality in the tropics (wet and dry season) can only be represented by defining date or heat unit specific “plant” and “kill” operations which are fixed for every year of simulation. In this paper, we discuss these shortcomings and present an alternative approach to automatically initiate annual growing cycles based on changes in soil moisture. Furthermore, we propose a logistic leaf area index (LAI) decline function which approaches a user-defined minimum LAI instead of using the default function, which is not considering the minimum LAI. The modified SWAT model was tested based on MODIS LAI and evapotranspiration data for the Santa Maria/Torto watershed in Central Brazil, covered mostly by Cerrado (savanna) vegetation. Our model results show that the modified model can reasonably represent seasonal dynamics of the Cerrado biome. However, since the proposed changes are process-based but also allow flexible model settings (e.g. the beginning of growing cycles based on a soil moisture threshold adjustable for plant/land cover types), the modified plant growth module should be useful for large parts of the model community.
    Keywords: Tropics ; Cerrado ; Leaf Area Index ; Evapotranspiration ; Modis ; SWAT ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
    Source: ScienceDirect Journals (Elsevier)
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  • 6
    Language: English
    In: Ecological modelling, 2013, Vol.269, pp.98-112
    Description: The Soil and Water Assessment Tool (SWAT) has been used for assessing the impact of land cover and land management changes on water resources for a wide range of scales and environmental conditions across the globe. However, originally designed for temperate regions, SWAT must be critically examined for its appropriate use in tropical watersheds. One major concern is the simulation of perennial tropical vegetation due to the absence of dormancy. While for temperate regions SWAT uses dormancy to terminate growing seasons of trees and perennials, seasonality in the tropics (wet and dry season) can only be represented by defining date or heat unit specific “plant” and “kill” operations which are fixed for every year of simulation. In this paper, we discuss these shortcomings and present an alternative approach to automatically initiate annual growing cycles based on changes in soil moisture. Furthermore, we propose a logistic leaf area index (LAI) decline function which approaches a user-defined minimum LAI instead of using the default function, which is not considering the minimum LAI. The modified SWAT model was tested based on MODIS LAI and evapotranspiration data for the Santa Maria/Torto watershed in Central Brazil, covered mostly by Cerrado (savanna) vegetation. Our model results show that the modified model can reasonably represent seasonal dynamics of the Cerrado biome. However, since the proposed changes are process-based but also allow flexible model settings (e.g. the beginning of growing cycles based on a soil moisture threshold adjustable for plant/land cover types), the modified plant growth module should be useful for large parts of the model community. ; p. 98-112.
    Keywords: Soil And Water Assessment Tool Model ; Cerrado ; Environmental Factors ; Land Cover ; Watersheds ; Dry Season ; Ecosystems ; Growing Season ; Temperate Zones ; Evapotranspiration ; Heat ; Dormancy ; Tropics ; Soil Water ; Perennials ; Land Management ; Trees ; Savannas ; Water Resources ; Leaf Area Index ; Moderate Resolution Imaging Spectroradiometer
    ISSN: 0304-3800
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 7
    Language: English
    In: Agriculture, Ecosystems and Environment, 2011, Vol.142(1), pp.1-5
    Keywords: Agriculture ; Environmental Sciences
    ISSN: 0167-8809
    E-ISSN: 1873-2305
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  • 8
    Language: English
    In: Agricultural Water Management, 31 January 2017, Vol.180, pp.191-193
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.agwat.2016.09.029 Byline: Martin Volk Author Affiliation: UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
    Keywords: Agriculture
    ISSN: 0378-3774
    E-ISSN: 1873-2283
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  • 9
    Language: English
    In: Agricultural Water Management, September 2016, Vol.175, pp.1-3
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.agwat.2016.06.013 Byline: Martin Volk Author Affiliation: UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
    Keywords: Agriculture
    ISSN: 0378-3774
    E-ISSN: 1873-2283
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  • 10
    In: PLoS ONE, 2016, Vol.11(8)
    Description: A number of concepts exist regarding how urbanization can be described as a process. Understanding this process that affects billions of people and its future development in a spatial manner is imperative to address related issues such as human quality of life. In the focus of spatially explicit studies on urbanization is typically a city, a particular urban region, an agglomeration. However, gaps remain in spatially explicit global models. This paper addresses that issue by examining the spatial dynamics of urban areas over time, for a full coverage of the world. The presented model identifies past, present and potential future hotspots of urbanization as a function of an urban area's spatial variation and age, whose relation could be depicted both as a proxy and as a path of urban development.
    Keywords: Research Article ; Earth Sciences ; Computer And Information Sciences ; Earth Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Research And Analysis Methods ; Physical Sciences ; People And Places ; Physical Sciences ; Medicine And Health Sciences
    E-ISSN: 1932-6203
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